sphinxcontrib-matlabdomain 0.21.4rc2

Sphinx "matlabdomain" extension

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sphinxcontrib-matlabdomain -- Sphinx domain for auto-documenting MATLAB
=======================================================================

This extension provides a `Sphinx <http://www.sphinx-doc.org/en/master/index.html>`_
*domain* for automatically generating doumentation from MATLAB source files.
It is modelled after the `Python autodoc <http://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html>`_.

The extension allows you to have your documentation and source files together
and use the powerful `Sphinx <http://www.sphinx-doc.org/en/master/index.html>`_
documentation tool. All your MATLAB file help text can be automatically
included in the your documentation and output as for instance HTML.

The extension works really well with `sphinx.ext.napoleon
<https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html>`_.

Recent `Changes <https://github.com/sphinx-contrib/matlabdomain/blob/master/CHANGES.rst>`_.


Usage
=====

The Python package must be installed with::

pip install sphinxcontrib-matlabdomain

In general, the usage is the same as for documenting Python code. The package
is tested with Python >= 3.8 and Sphinx >= 4.5.0.

For a Python 2 compatible version the package must be installed with::

pip install sphinxcontrib-matlabdomain==0.11.8


Configuration
-------------
In your Sphinx ``conf.py`` file add ``sphinxcontrib.matlab`` to the list of
extensions. ::

extensions = ['sphinxcontrib.matlab', 'sphinx.ext.autodoc']

For convenience the `primary domain <https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-primary_domain>`_
can be set to ``mat`` with.::

primary_domain = "mat"


Additional Configuration
~~~~~~~~~~~~~~~~~~~~~~~~

``matlab_src_dir``
In order for the Sphinx MATLAB domain to auto-document MATLAB source code,
set the config value of ``matlab_src_dir`` to an absolute path or a path
relative to the source directory. Currently only one MATLAB path can be
specified, but that folder and all the subfolders in that tree will be
searched.

``matlab_short_links``
Shorten all class, package and functions to the minimum length. This assumes
that everything is in the path as we would expect it in MATLAB. This will
resemble a more MATLAB-like presentation. If it is ``True`` is forces
``matlab_keep_package_prefix = False``. Further, it allows for much shorter
and cleaner references. Example, given a path to classes like
``target.subfolder.ClassFoo`` and ``[e-mail]``

* With ``False``::

:class:`target.subfolder.ClassFoo`

:class:`[e-mail]`

* With ``True``::

:class:`ClassFoo`

:class:`ClassFolder`

Default is ``False``. *Added in Version 0.19.0*.

``matlab_auto_link``
Automatically convert the names of known entities (e.g. classes, functions,
properties, methods) to links. Valid values are ``"basic"``
and ``"all"``.

* ``"basic"`` - Auto-links (1) known classes, functions, properties, or
methods that appear in docstring lines that begin with "See also" and any
subsequent lines before the next blank line (unknown names are wrapped in
double-backquotes), and (2) property and method names that appear in lists
under "<MyClass> Properties:" and "<MyClass> Methods:" headings in class
docstrings.

* ``"all"`` - Auto-links everything included with ``"basic"``, plus all known
classes and functions everywhere else they appear in any docstring, any
fully qualified (including class name) property or method names, any
names ending with "()" within class, property, or method docstrings that
match a method of the corresponding class, and any property or method names
in their own docstrings. Note that a non-breaking space before or after
a name will prevent auto-linking.

Default is ``None``. *Added in Version 0.20.0*.

``matlab_show_property_default_value``
Show property default values in the rendered document. Default is ``False``,
which is what MathWorks does in their documentation. *Added in Version
0.16.0*.

``matlab_class_signature``
Shows the constructor argument list in the class signature if ``True``.
Default is ``False``. *Added in Version 0.20.0*.

``matlab_keep_package_prefix``
Determines if the MATLAB package prefix ``+`` is displayed in the generated
documentation. Default is ``False``. When ``False``, packages are still
referred to in ReST using ``+pakage.+subpkg.func`` but the output will be
``pakage.subpkg.func()``. Forced to ``False`` if ``matlab_short_links`` is
``True``. *Added in Version 0.11.0*.

``matlab_src_encoding``
The encoding of the MATLAB files. By default, the files will be read as utf-8
and parsing errors will be replaced using ? chars. *Added in Version 0.9.0*.

If you want the closest to MATLAB documentation style, use ``matlab_short_links
= True`` and ``matlab_auto_link = "basic"`` or ``matlab_auto_link = "all"`` in
your ``conf.py`` file.


Roles and Directives
--------------------

Please see `Sphinx Domains <https://www.sphinx-doc.org/en/master/usage/restructuredtext/domains.html>`_ and
`sphinx.ext.autodoc
<http://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html>`_ for
documentation on the use of roles and directives. MATLAB code can be documented
using the following roles and directives:

==================================== ===========================================
Directive MATLAB object
==================================== ===========================================
``.. module:: foldername`` **folders, packages and namespaces**
``.. currentmodule:: foldername`` * set folder but do not link
``.. automodule:: foldername`` * auto-document
``:mod:`foldername``` * reference
``.. function:: funcname`` **function definition and signature**
``.. autofunction:: funcname()`` * auto-document
``:func:`funcname``` * reference
``.. script:: scriptname`` **script definition**
``.. autoscript:: scriptname`` * auto-document
``:scpt:`scriptname``` * reference
``.. class:: classname()`` **class definition and optional signature**
``.. autoclass:: classname`` * auto-document
``:class:`classname``` * reference
``.. method:: methname()`` **method definition and signature**
``.. automethod:: methname`` * auto-document
``:meth:`methname``` * reference
``.. staticmethod:: statmethname()`` **static method definition and signature**
``.. automethod:: statmethname`` * auto-document
``:meth:`methname``` * reference
``.. attribute:: attrname`` **property definition**
``.. autoattribute:: attrname`` * auto-document
``:attr:`attrname``` * reference
``.. application:: appname`` **application definition**
``.. autoapplication:: appname`` * auto-document
``:app:`appname``` * reference
==================================== ===========================================

Several options are available for auto-directives.

* ``:members:`` auto-document public members
* ``:show-inheritance:`` list bases
* ``:undoc-members:`` document members without docstrings
* ``:annotation:`` specifies attribute annotation instead of default

There are also several config values that can be set in ``conf.py`` that will
affect auto-docementation.

* ``autoclass_content`` can be set to ``class``, ``both`` or ``init``, which
determines which docstring is used for classes. The constructor docstring
is used when this is set to ``init``.
* ``autodoc_member_order`` can be set to ``alphabetical``, ``groupwise`` or
``bysource``.
* ``autodoc_default_flags`` can be set to a list of options to apply. Use
the ``no-flag`` directive option to disable this config value once.

.. note::

The module roles and directives create a psuedo namespace for MATLAB
objects, similar to a package. They represent the path to the folder
containing the MATLAB object. If no module is specified then Sphinx will
assume that the object is a built-in.

Example: given the following MATLAB source in folder ``test_data``::

classdef MyHandleClass < handle & my.super.Class
% a handle class
%
% :param x: a variable

%% some comments
properties
x % a property

% Multiple lines before a
% property can also be used
y
end
methods
function h = MyHandleClass(x)
h.x = x
end
function x = get.x(obj)
% how is this displayed?
x = obj.x
end
end
methods (Static)
function w = my_static_function(z)
% A static function in :class:`MyHandleClass`.
%
% :param z: input z
% :returns: w

w = z
end
end
end

Use the following to document::

Test Data
=========
This is the test data module.

.. automodule:: test_data

:mod:`test_data` is a really cool module.

My Handle Class
---------------
This is the handle class definition.

.. autoclass:: MyHandleClass
:show-inheritance:
:members:

In version 0.19.0 the ``.. automodule::`` directive can also take a ``.`` as
argument, which allows you to document classes or functions in the root of
``matlab_src_dir``.


Module Index
------------

Since version 0.10.0 the *MATLAB Module Index* should be linked to with::

`MATLAB Module Index <mat-modindex.html>`_

Older versions, used the *Python Module Index*, which was linked to with::

:ref:`modindex`


Documenting Python and MATLAB sources together
==============================================

Since version 0.10.0 MATLAB and Python sources can be (auto-)documented in the same
Sphinx documentation. For this to work, do not set the `primary domain <https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-primary_domain>`_.

Instead use the ``mat:`` prefix before the desired directives::

.. automodule:: func
.. autofunction:: func.main

.. mat:automodule:: matsrc
.. mat:autofunction:: matsrc.func


Online Demo
===========

.. warning::

The online demo is highly outdated!

The test docs in the repository are online here:
http://bwanamarko.alwaysdata.net/matlabdomain/

.. note::

Sphinx style markup are used to document parameters, types, returns and
exceptions. There must be a blank comment line before and after the
parameter descriptions.


Users
=====

* `Cantera <http://cantera.github.io/docs/sphinx/html/compiling/dependencies.html?highlight=matlabdomain>`_
* `CoSMo MVPA <http://cosmomvpa.org/download.html?highlight=matlabdomain#developers>`_
* `The Cobra Toolbox <https://opencobra.github.io/cobratoolbox/stable/index.html#>`_
* `The RepLAB Toolbox <https://replab.github.io/replab>`_


Citation
========
.. image:: https://zenodo.org/badge/105161090.svg
:target: https://zenodo.org/badge/latestdoi/105161090